PDB-4gnx: Structure of U. maydis Replication protein A bound to ssDNA

ID or keywords:

Entry

Database: PDB / ID: 4gnx

Title

Structure of U. maydis Replication protein A bound to ssDNA

Components

(Putative uncharacterized protein) x 3
DNA (25-MER)

Keywords

DNA BINDING PROTEIN/DNA / ssDNA binding / DNA BINDING PROTEIN-DNA complex

Function / homology

Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / DNA / DNA (> 10) / : / : / :

Function and homology information

Biological species

Ustilago maydis (corn smut)
synthetic (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Pavletich, N.P. / Fan, J.

Citation

Journal: To be Published
Title: Structure of
Authors: Pavletich, N.P. / Fan, J.

History

Deposition	Aug 17, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2013	Group: Structure summary
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gnx.cif.gz	559.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4gnx.ent.gz	460.7 KB	Display	PDB format
PDBx/mmJSON format	4gnx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gn/4gnx ftp://data.pdbj.org/pub/pdb/validation_reports/gn/4gnx	HTTPS FTP

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Related structure data

Similar structure data	4gop-1 4a7p-d 5mbt-d 1ek2-d 4z1i-1 5lwq-d 4m8r-d 6o1y-d 1s5j-d 4q5v-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Thymine Dimers
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Enhanceosome
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RecA and Rad51
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Cascade and CRISPR
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Expressome
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Oct and Sox Transcription Factors
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Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
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DNA Methyltransferase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
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#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
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Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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lac Repressor
similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)
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similarity (1)

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

X: Putative uncharacterized protein

Y: Putative uncharacterized protein

Z: Putative uncharacterized protein

K: DNA (25-MER)

L: DNA (25-MER)

hetero molecules

192 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

K: DNA (25-MER)

hetero molecules

defined by author&software
96.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

X: Putative uncharacterized protein

Y: Putative uncharacterized protein

Z: Putative uncharacterized protein

L: DNA (25-MER)

hetero molecules

defined by author&software
96.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.100, 91.400, 114.600
Angle α, β, γ (deg.)	90.000, 97.800, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 2

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	VAL	VAL	A	A	3 - 67	3 - 67
2	1	1	LYS	LYS	VAL	VAL	X	D	3 - 67	3 - 67
1	2	1	PHE	PHE	ILE	ILE	A	A	74 - 79	74 - 79
2	2	1	PHE	PHE	ILE	ILE	X	D	74 - 79	74 - 79
1	1	2	ASP	ASP	ASP	ASP	A	A	92 - 112	92 - 112
2	1	2	ASP	ASP	ASP	ASP	X	D	92 - 112	92 - 112
1	1	3	ASN	ASN	GLU	GLU	B	B	46 - 60	7 - 21
2	1	3	ASN	ASN	GLU	GLU	Y	E	46 - 60	7 - 21
1	2	3	ILE	ILE	ASP	ASP	B	B	69 - 112	30 - 73
2	2	3	ILE	ILE	ASP	ASP	Y	E	69 - 112	30 - 73
1	1	4	VAL	VAL	ARG	ARG	B	B	153 - 175	114 - 136
2	1	4	VAL	VAL	ARG	ARG	Y	E	153 - 175	114 - 136
1	1	5	ILE	ILE	ARG	ARG	C	C	182 - 208	3 - 29
2	1	5	ILE	ILE	ARG	ARG	Z	F	182 - 208	3 - 29
1	2	5	LEU	LEU	LYS	LYS	C	C	219 - 297	40 - 118
2	2	5	LEU	LEU	LYS	LYS	Z	F	219 - 297	40 - 118
1	1	6	TYR	TYR	LEU	LEU	C	C	298 - 327	119 - 148
2	1	6	TYR	TYR	LEU	LEU	Z	F	298 - 327	119 - 148
1	2	6	LYS	LYS	ASN	ASN	C	C	341 - 431	162 - 252
2	2	6	LYS	LYS	ASN	ASN	Z	F	341 - 431	162 - 252
1	1	7	GLY	GLY	ASN	ASN	C	C	441 - 447	262 - 268
2	1	7	GLY	GLY	ASN	ASN	Z	F	441 - 447	262 - 268
1	1	8	MET	MET	TYR	TYR	C	C	448 - 486	269 - 307
2	1	8	MET	MET	TYR	TYR	Z	F	448 - 486	269 - 307
1	2	8	TYR	TYR	LYS	LYS	C	C	523 - 586	344 - 407
2	2	8	TYR	TYR	LYS	LYS	Z	F	523 - 586	344 - 407
1	3	8	VAL	VAL	VAL	VAL	C	C	596 - 606	417 - 427
2	3	8	VAL	VAL	VAL	VAL	Z	F	596 - 606	417 - 427
1	1	9	TYR	TYR	ARG	ARG	C	C	487 - 522	308 - 343
2	1	9	TYR	TYR	ARG	ARG	Z	F	487 - 522	308 - 343
1	2	9	ZN	ZN	ZN	ZN	C	I	701
2	2	9	ZN	ZN	ZN	ZN	Z	J	701
1	1	10	ASP	ASP	MET	MET	C	C	607 - 623	428 - 444
2	1	10	ASP	ASP	MET	MET	Z	F	607 - 623	428 - 444

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	Putative uncharacterized protein Mass: 12175.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (corn smut) / Strain: 521 / FGSC 9021 / Gene: UM04165.1 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4P6U8
#2: Protein	Putative uncharacterized protein Mass: 15248.052 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (corn smut) / Strain: 521 / FGSC 9021 / Gene: UM02579.1 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4PBD4
#3: Protein	Putative uncharacterized protein Mass: 49837.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ustilago maydis (corn smut) / Strain: 521 / FGSC 9021 / Gene: UM05156.1 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4P407
#4: DNA chain	DNA (25-MER) Mass: 18814.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.68 %

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 1 Å

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.8→35 Å / Num. all: 39488 / Num. obs: 37317 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / R_merge(I) obs: 0.068 / R_sym value: 0.065 / Χ²: 1.214 / Net I/σ(I): 11.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.9	2.5	0.574	3776	1.474	1	97.4
2.9-3.02	2.5	0.391	3850	1.329	1	97.4
3.02-3.15	2.4	0.261	3839	1.249	1	97.5
3.15-3.32	2.4	0.172	3800	1.158	1	96.8
3.32-3.53	2.4	0.108	3812	1.189	1	96.5
3.53-3.8	2.4	0.076	3748	1.131	1	95.6
3.8-4.18	2.4	0.051	3689	1.122	1	93.4
4.18-4.78	2.3	0.036	3660	1.161	1	92.2
4.78-6.02	2.3	0.034	3599	1.178	1	90.6
6.02-35	2.4	0.025	3544	1.106	1	87.5

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.6.0117	refinement
PDB_EXTRACT	3.11	data extraction
ADSC	Quantum	data collection
DENZO		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.882 / Occupancy max: 1 / Occupancy min: 1 / SU B: 39.566 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2783	1398	4 %	RANDOM
R_work	0.2193	-	-	-
obs	0.2217	34942	88.29 %	-
all	-	33544	-	-

Solvent computation

Ion probe radii: 1 Å / Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 207.34 Å² / B_iso mean: 70.016 Å² / B_iso min: 12.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.04 Å²	0 Å²	-1.11 Å²
2-	-	2.73 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10448	900	2	0	11350

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	11623
X-RAY DIFFRACTION	r_angle_refined_deg	1.331	1.893	15908
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.665	5	1314
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.955	24.44	536
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.016	15	1826
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.872	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1745
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	8566

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	68	TIGHT POSITIONAL	0.04	0.05
1	A	245	MEDIUM POSITIONAL	0.04	0.5
1	A	284	TIGHT THERMAL	2.44	99
1	A	245	MEDIUM THERMAL	2.56	99
2	A	77	MEDIUM POSITIONAL	0.05	0.5
2	A	84	TIGHT THERMAL	1.26	99
2	A	77	MEDIUM THERMAL	1.41	99
3	B	224	MEDIUM POSITIONAL	0.04	0.5
3	B	236	TIGHT THERMAL	1.57	99
3	B	224	MEDIUM THERMAL	2.89	99
4	B	103	MEDIUM POSITIONAL	0.05	0.5
4	B	92	TIGHT THERMAL	1.87	99
4	B	103	MEDIUM THERMAL	1.88	99
5	C	437	MEDIUM POSITIONAL	0.04	0.5
5	C	424	TIGHT THERMAL	2.94	99
5	C	437	MEDIUM THERMAL	3.38	99
6	C	465	MEDIUM POSITIONAL	0.03	0.5
6	C	484	TIGHT THERMAL	9.15	99
6	C	465	MEDIUM THERMAL	10.24	99
7	C	6	MEDIUM POSITIONAL	0.05	0.5
7	C	28	TIGHT THERMAL	27.14	99
7	C	6	MEDIUM THERMAL	29.38	99
8	C	455	MEDIUM POSITIONAL	0.04	0.5
8	C	456	TIGHT THERMAL	3.83	99
8	C	455	MEDIUM THERMAL	3.79	99
9	C	152	MEDIUM POSITIONAL	0.35	0.5
9	C	144	TIGHT THERMAL	2.16	99
9	C	152	MEDIUM THERMAL	2.61	99
10	C	63	MEDIUM POSITIONAL	0.05	0.5
10	C	68	TIGHT THERMAL	0.97	99
10	C	63	MEDIUM THERMAL	2.05	99

LS refinement shell

Resolution: 2.8→2.871 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	76	-
R_work	0.316	2075	-
all	-	2151	-
obs	-	-	76.77 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.6419	3.7556	-1.3755	6.6683	-0.8755	4.4864	-0.1721	-0.1632	-0.4042	-0.1599	-0.0413	0.1429	0.4731	-0.2275	0.2135	0.1277	0.0059	0.0119	0.0769	0.0537	0.1217	-6.82	-11.354	44.334
2	7.9901	0.8962	0.1521	5.923	0.0265	2.7214	-0.0314	0.0592	0.7159	-0.0097	-0.1109	0.5649	-0.3115	-0.3316	0.1422	0.0668	0.0138	-0.0195	0.1231	-0.0035	0.1144	-10.336	10.223	37.443
3	5.2565	2.035	-0.8833	4.915	-2.0764	8.2833	-0.0017	0.0756	0.0436	-0.0161	0.1023	-0.5478	-0.1951	0.8121	-0.1006	0.0197	0.0194	0.0212	0.329	-0.071	0.2133	34.645	0.114	38.259
4	6.0101	0.8091	-0.9722	6.0131	-0.3811	4.7335	0.3006	0.499	-0.3081	-0.6302	-0.4738	-0.2	0.4118	0.045	0.1733	0.6076	0.0548	0.0827	0.4604	0.0183	0.3091	29.105	-3.69	11.682
5	3.5896	-0.3074	2.0295	1.4683	-1.0531	4.5425	-0.0613	0.4024	0.1634	-0.6694	0.0321	-0.0072	0.0334	0.0519	0.0293	0.3683	-0.0448	-0.006	0.1225	0.006	0.0691	-3.858	11.031	15.257
6	15.7024	-1.4111	2.97	2.9346	-0.7002	7.3928	0.8162	1.2163	-0.337	-0.8319	-0.1381	-0.2524	0.7756	0.5006	-0.678	0.4967	0.087	-0.0587	0.411	-0.0123	0.126	-17.781	13.701	-9.248
7	7.515	-3.5585	-1.1837	5.0126	1.3205	4.8048	-0.0516	0.0446	-0.6144	0.2944	-0.0836	-0.4904	0.7822	-0.1582	0.1352	0.2315	-0.062	-0.0604	0.0227	0.0134	0.2618	17.214	-11.723	58.222
8	7.6785	-0.2921	0.7278	4.537	-0.3059	3.7104	-0.1476	-0.4274	0.596	0.2021	0.0733	-0.6284	-0.242	-0.023	0.0743	0.0642	0.0549	-0.0599	0.0845	-0.071	0.1426	20.161	9.655	65.698
9	5.427	-2.4101	-0.82	5.2748	2.3457	9.4492	-0.1561	0.1036	0.1863	-0.0932	-0.0508	0.203	-0.3413	0.0091	0.2069	0.0214	0.0025	-0.014	0.0606	0.0383	0.1122	-24.813	-0.463	64.365
10	3.7811	-1.4926	-0.2902	11.0322	-1.1242	3.6532	-0.3177	-0.3875	0.0658	1.4632	0.4227	-0.0164	-0.0426	0.1854	-0.1049	0.8166	0.3408	0.1125	0.3729	-0.052	0.1926	-21.469	-4.455	90.2
11	3.2116	1.0051	2.5122	1.6731	0.967	4.8409	0.0242	-0.5269	0.3346	0.6318	-0.1105	-0.0276	-0.0982	-0.6007	0.0863	0.4701	0.1069	-0.0968	0.4156	-0.0729	0.1484	13.524	9.902	87.819
12	11.4481	3.6916	3.8625	8.1409	-0.4823	7.7761	0.5964	-1.3027	0.0097	1.0376	-0.162	0.4766	0.5744	-0.4661	-0.4344	0.4657	-0.051	-0.0289	0.4672	0.0996	0.1005	27.684	13.281	112.157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 112
2	X-RAY DIFFRACTION	2	B	46 - 175
3	X-RAY DIFFRACTION	3	C	182 - 297
4	X-RAY DIFFRACTION	4	C	298 - 447
5	X-RAY DIFFRACTION	5	C	448 - 487
6	X-RAY DIFFRACTION	5	C	522 - 623
7	X-RAY DIFFRACTION	6	C	488 - 521
8	X-RAY DIFFRACTION	6	C	701
9	X-RAY DIFFRACTION	7	X	1 - 112
10	X-RAY DIFFRACTION	8	Y	46 - 175
11	X-RAY DIFFRACTION	9	Z	182 - 297
12	X-RAY DIFFRACTION	10	Z	298 - 422
13	X-RAY DIFFRACTION	11	Z	448 - 487
14	X-RAY DIFFRACTION	11	Z	522 - 623
15	X-RAY DIFFRACTION	12	Z	488 - 521
16	X-RAY DIFFRACTION	12	Z	701

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